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Structure of Phosphopantetheine adenylyltransferase (PPAT) from Enterobacter spp. with the expression tag bound in the substrate binding site of a neighbouring molecule at 2.39 A resolution.
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 8I8I
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7 298 BIS-TRIS propane pH 7.0, Sodium citrate tribasic dihydrate
Crystal Properties Matthews coefficient Solvent content 2.71 54.72
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 137.919 α = 90 b = 78.618 β = 93.118 c = 106.981 γ = 90
Symmetry Space Group C 1 2 1
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 100 PIXEL DECTRIS PILATUS3 2M 2022-09-24 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 SYNCHROTRON ESRF BEAMLINE ID23-2 0.8731 ESRF ID23-2
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.39 56.49 96 0.118 0.118 0.981 5.3 2.1 43366
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Rpim I (All) CC (Half) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 1 2.39 2.48 97.8 0.57 0.568 0.594 1.8 2.1
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Resolution (High) Resolution (Low) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Work (Depositor) R-Work (DCC) R-Free (Depositor) R-Free (DCC) Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT FREE R-VALUE 2.39 42.666 43349 893 95.403 0.223 0.2224 0.2268 0.2405 0.2464 42.57
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] 1.201 0.578 1.257 -2.506
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.308 r_dihedral_angle_6_deg 14.854 r_dihedral_angle_3_deg 13.342 r_lrange_other 12.298 r_lrange_it 12.295 r_scangle_it 6.954 r_scangle_other 6.954 r_mcangle_it 6.049 r_mcangle_other 6.048 r_dihedral_angle_1_deg 5.922
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 15.308 r_dihedral_angle_6_deg 14.854 r_dihedral_angle_3_deg 13.342 r_lrange_other 12.298 r_lrange_it 12.295 r_scangle_it 6.954 r_scangle_other 6.954 r_mcangle_it 6.049 r_mcangle_other 6.048 r_dihedral_angle_1_deg 5.922 r_scbond_it 4.299 r_scbond_other 4.298 r_mcbond_it 3.804 r_mcbond_other 3.804 r_angle_refined_deg 1.39 r_angle_other_deg 0.489 r_nbd_other 0.249 r_symmetry_nbd_refined 0.216 r_symmetry_nbd_other 0.2 r_nbd_refined 0.199 r_symmetry_xyhbond_nbd_refined 0.189 r_xyhbond_nbd_refined 0.188 r_nbtor_refined 0.168 r_ncsr_local_group_10 0.134 r_ncsr_local_group_2 0.127 r_ncsr_local_group_11 0.126 r_ncsr_local_group_13 0.12 r_ncsr_local_group_12 0.119 r_ncsr_local_group_6 0.118 r_ncsr_local_group_3 0.11 r_ncsr_local_group_15 0.11 r_ncsr_local_group_8 0.108 r_symmetry_xyhbond_nbd_other 0.104 r_ncsr_local_group_5 0.102 r_ncsr_local_group_1 0.1 r_ncsr_local_group_7 0.099 r_ncsr_local_group_14 0.098 r_ncsr_local_group_4 0.082 r_ncsr_local_group_9 0.082 r_symmetry_nbtor_other 0.077 r_chiral_restr 0.067 r_xyhbond_nbd_other 0.03 r_bond_refined_d 0.006 r_gen_planes_refined 0.006 r_bond_other_d 0.001 r_gen_planes_other 0.001
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 7662 Nucleic Acid Atoms Solvent Atoms 574 Heterogen Atoms 68
Software Software Software Name Purpose REFMAC refinement MxCuBE data collection XDS data reduction autoPROC data scaling MOLREP phasing Coot model building